Marker associated with resistance to smut in plant belonging to genus Saccharum, and use thereof

ABSTRACT

The present invention relates to a marker associated with resistance to smut which is a quantitative trait of sugarcane. Specifically, a marker associated with resistance to sugarcane smut, which consists of a continuous nucleic acid region existing in a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 1 and the nucleotide sequence shown in SEQ ID NO: 14 or a different similar region, is provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Divisional of U.S. application Ser. No. 14/113,539 filed Oct. 23, 2013, which is a National Stage of International Application No. PCT/JP2012/060671, filed Apr. 20, 2012, which claims priority to Japanese Patent Application No. 2011-101050, filed Apr. 28, 2011, and to Japanese Patent Application No. 2012-094995, filed Apr. 18, 2012, the contents of all of which are incorporated herein by reference in their entirety.

TECHNICAL FIELD

The present invention relates to a marker associated with resistance to smut whereby a sugarcane line resistant to smut can be selected, and a method for use thereof.

BACKGROUND ART

Sugarcane has been cultivated as a raw material for sugar, liquor, and the like for edible use. In addition, sugarcane has been used as, for example, a raw material for biofuel in a variety of industrial fields. Under such circumstances, there is a need to develop novel sugarcane varieties having desirable characteristics (e.g., sugar content, enhanced vegetative capacity, sprouting capacity, disease resistance, insect resistance, cold resistance, an increase in leaf blade length, an increase in leaf area, and an increase in stalk length).

In general, the following three ways may be used for identification of a plant variety/line: “characteristics comparison” for comparison of characteristics data, “comparison during cultivation” for comparison of plants cultivated under the same conditions, and “DNA assay” for DNA analysis. There are many problems in line identification with characteristics comparison or comparison during cultivation, including reduction of precision due to differences in cultivation conditions, lengthy duration of field research that requires a number of steps, and the like. In particular, since sugarcane plants are much larger than other graminaceous crops such as rice and maize, it has been difficult to conduct line identification based on field research.

In addition, in order to identify a variety resistant to a certain disease, an inoculation test is carried out using a causative microorganism of a disease after long-term cultivation of sugarcane, and then disease resistance data are collected by observing lesions and the like. However, transmission of the causative microorganism to an external environment must be securely prevented when the test is carried out, and thus it is necessary to provide, for example, facilities such as a large-scale special-purpose greenhouse, a special-purpose field or isolation facility from an external environment. Further, for creation of a novel sugarcane variety, first, tens of thousands of hybrids are created via crossing, followed by seedling selection and stepwise selection of desirable excellent lines. Eventually, 2 or 3 types of novel varieties having desired characteristics can be obtained. As described above, for creation of a novel sugarcane variety, it is necessary to cultivate and evaluate an enormous number of lines, and it is also necessary to prepare the above large-scale greenhouse or field and undertake highly time-consuming efforts.

Therefore, it has been required to develop a method for identifying a sugarcane line having disease resistance with the use of markers present in the sugarcane genome. In particular, upon creation of a novel sugarcane variety, if excellent markers could be used to examine a variety of characteristics, the above problems particular to sugarcane would be resolved, and the markers would be able to serve as very effective tools. However, since sugarcane plants have a large number of chromosomes (approximately 100 to 130) due to higher polyploidy, the development of marker technology has been slow. In the case of sugarcane, although the USDA reported genotyping with the use of SSR markers (Non-Patent Literature 1), the precision of genotyping is low because of the small numbers of markers and polymorphisms in each marker. In addition, the above genotyping is available only for American/Australian varieties, and therefore it cannot be used for identification of the major varieties cultivated in Japan, Taiwan, India, and other countries or lines that serve as useful genetic resources.

In addition, Non-Patent Literature 2 suggests the possibility that a sugarcane genetic map can be created by increasing the number of markers, comparing individual markers in terms of a characteristic relationship, and verifying the results. However, in Non-Patent Literature 2, an insufficient number of markers are disclosed and markers linked to desired characteristics have not been found.

Meanwhile, as a marker associated with disease resistance, a marker associated with black root rot resistance in sugar beet disclosed in Patent Literature 1 is known. In addition, a technique of selecting a Zea mays variety using a maker linked to a desired trait is disclosed in Patent Literature 2.

The level of infectiousness of the causative microorganism of sugarcane smut is high, and therefore the onset of smut quickly results in the infection of the entire field. Crops of sugarcane affected with smut cannot be used as raw material for sugar production, and even they die. Therefore, the development of smut will cause a significant decline in yield within the following year or later. Damage due to smut has been reported in more than 28 countries, including Brazil, the U.S., Australia, China, and Indonesia. Smut can be prevented by sterilization treatment prior to planting; however, preventive effects are limited to the period of early growth. Thus, cultivation of a sugarcane variety imparted with smut resistance has been awaited.

CITATION LIST Non-Patent Literature

-   Non-Patent Literature 1: Maydica 48(2003)319-329 “Molecular     genotyping of sugarcane clones with microsatellite DNA markers” -   Non-Patent Literature 2: Nathalie Piperidis et al., Molecular     Breeding, 2008, Vol. 21, 233-247

Patent Literature

-   Patent Literature 1: WO 2007/125958 -   Patent Literature 2: JP Patent Publication (Kokai) No. 2010-516236 A

SUMMARY OF INVENTION Technical Problem

In view of the above, an object of the present invention is to provide a marker associated with resistance to smut, which is a quantitative trait of sugarcane.

Solution to Problem

In order to achieve the object, the present inventors conducted intensive studies. The present inventors prepared many sugarcane plant markers and carried out linkage analysis of quantitative traits along with such markers for hybrid progeny lines. Accordingly, the present inventors found markers linked to quantitative traits such as smut resistance. This has led to the completion of the present invention.

The present invention encompasses the following.

(1) A marker associated with resistance to sugarcane smut, which consists of a continuous nucleic acid region existing in a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 1 and the nucleotide sequence shown in SEQ ID NO: 14, a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 15 and the nucleotide sequence shown in SEQ ID NO: 22, a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 23 and the nucleotide sequence shown in SEQ ID NO: 32, a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 33 and the nucleotide sequence shown in SEQ ID NO: 51, a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 52 and the nucleotide sequence shown in SEQ ID NO: 62, a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 63 and the nucleotide sequence shown in SEQ ID NO: 72, or a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 73 and the nucleotide sequence shown in SEQ ID NO: 85 of a sugarcane chromosome.

(2) The marker associated with resistance to sugarcane smut according to (1), wherein the continuous nucleic acid region comprises any nucleotide sequence selected from the group consisting of the nucleotide sequences shown in SEQ ID NOS: 1 to 85 or a part of the nucleotide sequence.

(3) The marker associated with resistance to sugarcane smut according to (1), wherein the continuous nucleic acid region is located at a position in a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 5 and the nucleotide sequence shown in SEQ ID NO: 9, a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 18 and the nucleotide sequence shown in SEQ ID NO: 22, a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 25 and the nucleotide sequence shown in SEQ ID NO: 32, a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 33 and the nucleotide sequence shown in SEQ ID NO: 42, a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 57 and the nucleotide sequence shown in SEQ ID NO: 59, a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 64 and the nucleotide sequence shown in SEQ ID NO: 66, or a region sandwiched between the nucleotide sequence shown in SEQ ID NO: 72 and the nucleotide sequence shown in SEQ ID NO: 80 of a sugarcane chromosome.

(4) A method for producing a sugarcane line having improved smut resistance comprising: a step of extracting a chromosome of a progeny plant obtained from parent plants, at least one of which is a sugarcane plant, and/or a chromosome of a parent sugarcane plant; and a step of determining the presence or absence of the marker associated with resistance to sugarcane smut according to any one of (1) to (3) in the obtained chromosome.

(5) The method for producing a sugarcane line according to (4), wherein a DNA chip comprising a probe corresponding to the marker associated with resistance to sugarcane smut is used in the determination step.

(6) The method for producing a sugarcane line according to (4), wherein the progeny plant is in the form of seeds or a young seedling and the chromosome is extracted from the seeds or the young seedling.

This specification includes part or all of the contents as disclosed in the specification and/or drawings of Japanese Patent Application Nos. 2011-101050 and 2012-94995, which are priority documents of the present application.

Advantageous Effects of Invention

According to the present invention, a novel marker associated with resistance to sugarcane smut linked to a sugarcane quantitative trait such as smut resistance can be provided. With the use of the marker associated with resistance to sugarcane smut of the present invention, smut resistance of a line obtained by crossing sugarcane lines can be tested. Thus, a sugarcane line characterized by improved smut resistance can be identified at a very low cost.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 schematically shows the process of production of a DNA microarray used for acquisition of sugarcane chromosome markers.

FIG. 2 schematically shows a step of signal detection with the use of a DNA microarray.

FIG. 3 is a characteristic chart showing data on smut resistance examined on Jun. 23, 2010, for sugarcane variety/line groups used in the Examples.

FIG. 4 is a characteristic chart showing data on smut resistance examined on Jul. 21, 2010, for sugarcane variety/line groups used in the Examples.

FIG. 5 is a characteristic chart showing data on smut resistance examined on Aug. 18, 2010, for sugarcane variety/line groups used in the Examples.

FIG. 6 is a characteristic chart showing data on smut resistance examined on Sep. 2, 2010, for sugarcane variety/line groups used in the Examples.

FIG. 7 is a characteristic chart showing QTL analysis results regarding smut resistance (the 5th linkage group in NiF8).

FIG. 8 is a characteristic chart showing QTL analysis results regarding smut resistance (the 17th linkage group in NiF8).

FIG. 9 is a characteristic chart showing QTL analysis results regarding smut resistance (the 40th linkage group in NiF8).

FIG. 10 is a characteristic chart showing QTL analysis results regarding smut resistance (the 1st linkage group in Ni9).

FIG. 11 is a characteristic chart showing QTL analysis results regarding smut resistance (the 13th linkage group in Ni9).

FIG. 12 is a characteristic chart showing QTL analysis results regarding smut resistance (the 14th linkage group in Ni9).

FIG. 13 is a characteristic chart showing signal levels of N802870 for individual lines.

FIG. 14 is a characteristic chart showing signal levels of N827136 for individual lines.

FIG. 15 is a characteristic chart showing signal levels of N812680 for individual lines.

FIG. 16 is a characteristic chart showing signal levels of N916081 for individual lines.

FIG. 17 is a characteristic chart showing signal levels of N919839 for individual lines.

FIG. 18 is a characteristic chart showing signal levels of N918761 for individual lines.

FIG. 19 is a characteristic chart showing signal levels of N901160 for individual lines.

DESCRIPTION OF EMBODIMENTS

The marker associated with resistance to sugarcane smut and the method for using the same according to the present invention are described below. In particular, a method for producing a sugarcane line using a marker associated with resistance to sugarcane smut is described.

<Markers Associated with Resistance to Sugarcane Smut>

The marker associated with resistance to sugarcane smut of the present invention corresponds to a specific region present on a sugarcane chromosome and is linked to a causative gene (or a group of causative genes) for a trait characterized by smut resistance. Thus, it can be used to identify a trait characterized by smut resistance. Specifically, it is possible to determine that a progeny line obtained using a known sugarcane line is a line having a trait characterized by the improvement of smut resistance by confirming the presence or absence of the marker associated with resistance to sugarcane smut in such progeny line. In the present invention, the term “smut” refers to a disease characterized by lesion formation due to infection with a microorganism of the genus Ustilago. One example of a microorganism of the genus Ustilago is Ustilago scitaminea.

In addition, the term “marker associated with resistance to sugarcane smut” refers to both a marker linked to a trait characterized by the improvement of smut resistance and a marker linked to a trait characterized by the reduction of smut resistance. For example, if the presence of the former marker in a certain sugarcane variety is confirmed, it is possible to determine that the variety has improved smut resistance. Further, if the presence of the former marker and the absence of the latter marker in a certain sugarcane variety are confirmed, it is possible to determine that the variety has improved smut resistance with high accuracy. It is also possible to determine that a certain sugarcane variety has improved smut resistance by confirming only the absence of the latter marker.

The term “sugarcane” used herein refers to a plant belonging to the genus Saccharum of the family Poaceae. In addition, the term “sugarcane” includes so-called noble cane (scientific name: Saccharum officinarum) and wild cane (scientific name: Saccharum spontaneum), Saccharum barberi, Saccharum sinense, and the earlier species of Saccharum officinarum (Saccharum robustum). The term “known sugarcane variety/line” is not particularly limited. It includes any variety/line available in Japan and any variety/line available outside Japan. Examples of sugarcane varieties cultivated in Japan include, but are not limited to, Ni1, NiN2, NiF3, NiF4, NiF5, Nib, NiN7, NiF8, Ni9, NiTn10, Ni11, Ni12, Ni14, Ni15, Ni16, Ni17, NiTn19, NiTn20, Ni22, and Ni23. Examples of main sugarcane varieties used in Japan described herein include, but are not limited to, NiF8, Ni9, NiTn10, and Ni15. In addition, examples of main sugarcane varieties that have been introduced into Japan include, but are not limited to, F177, Nco310, and F172.

In addition, a progeny line may be a line obtained by crossing a mother plant and a father plant of the same species, each of which is a sugarcane variety/line, or it may be a hybrid line obtained from parent plants when one thereof is a sugarcane variety/line and the other is a closely related variety/line (Erianthus arundinaceus). In addition, a progeny line may be obtained by so-called backcrossing.

The marker associated with resistance to sugarcane smut of the present invention has been newly identified by QTL (Quantitative Trait Loci) analysis using a genetic linkage map containing 3004 markers and 4569 markers originally obtained from sugarcane chromosomes, and sugarcane smut resistance data. In addition, many genes are presumably associated with sugarcane smut resistance, which is a quantitative trait characterized by a continuous distribution of sugarcane smut resistance. That is, sugarcane smut resistance is evaluated based on the incidence of smut characterized by such continuous distribution. For QTL analysis, the QTL Cartographer gene analysis software (Wang S., C. J. Basten, and Z.-B. Zeng (2010); Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, N.C.) is used, and the analysis is carried out by the composite interval mapping (CIM) method.

Specifically, seven relevant regions included in the above genetic linkage map with LOD scores equivalent to or exceeding a given threshold (e.g., 2.5) have been found by QTL analysis described above. That is, the following 7 regions have been specified: an approximately 18.7-cM (centimorgan) region including the relevant region, an approximately 39.2-cM region including the relevant region, an approximately 19.2-cM region including the relevant region, an approximately 32.0-cM region including the relevant region, an approximately 39.5-cM region including the relevant region, an approximately 53.4-cM region including the relevant region, and an approximately 38.0-cM region including the relevant region. The term “morgan (M)” used herein refers to a unit representing the relative distance between genes on a chromosome, and it is expressed by the percentage of the crossover rate. In a case of a sugarcane chromosome, 1 cM corresponds to approximately 2000 kb. In addition, it is suggested that a causative gene (or a group of causative genes) for a trait that causes the improvement of smut resistance could be present at the peak positions or in the vicinity thereof.

The 18.7-cM region is a region that comprises 14 types of markers listed in table 1 below in the order shown in table 1 and is linked to a trait characterized by the reduction of smut resistance.

TABLE 1 Nucleotide Linkage Marker sequence Signal SEQ group name information threshold ID NO: NiF8_5 N827337 CCTCGTCATGC 1,000 SEQ ID ACCCGTGCCTC NO: 1 TTCTTCCTCTT GCTGTTGCTCC TCCTCC N802879 GGAATTGTTGT 1,000 SEQ ID AGATTTGTTTT NO: 2 GTGATGGAAAG ATCATACCTCA GCTACAAGAAG TAAATATCCTT TTCCA N804818 GGCATTAGAAG 1,000 SEQ ID AAAGGTGGAAG NO: 3 AATAAGGTTTG AGCCCTTATTT ATTTGCTTTGG TGATGGAT N816296 CCATTCTACTT 1,000 SEQ ID CTACCAACCAT NO: 4 AAAACAGGAGG AGCATGCATGC ACATGC N804607 ATTGCTTGCTC 1,000 SEQ ID GCTGCAACTTG NO: 5 GGCCATGTTTA GTTCCTCGAAT TTGAGT N802870 AGTGAAGAGAT 1,500 SEQ ID TGGATTTCTAG NO: 6 GGTTACTTTAT AAAGTGTCAAC ACCTTAGATCT GTTTTTTAGT N813249 GGCCGGCACGA 1,500 SEQ ID GCATCAGGGTC NO: 7 AAGACTCAAGA GCTCAAGTGCT TGCTTT N813609 TACTTTGTCTC 1,000 SEQ ID GTTCCAGTAGT NO: 8 CCATCAAGCAA GCCTCGTACAC AAGTCC N815502 TGCACTGGGGA 1,000 SEQ ID TACCAGTTGAG NO: 9 TTGATTGCACA ACTTGCGCTAC ACCATG N815101 GCCGCCTGATG 1,000 SEQ ID GAAACGGTCGT NO: 10 CGCATCCAAAG ACGCACATGGT TTAGCA N823481 AGTACCTGTTC 1,000 SEQ ID TGCTGCACTAC NO: 11 ATAACAGTACT TTTCAGTGAAC GAACAGTGTTT TC N801028 AGCGGATAGCG 1,500 SEQ ID CTAGCATGTCA NO: 12 TTCTCTCCCCT CGCTAGCACGT TATTCC N810798 GTTGCGGCGTG 1,500 SEQ ID TGTTGATGATG NO: 13 TAAAGAATACT CGTCCGTGAGA AATTATCA N821515 ACGTGACGACG 1,000 SEQ ID ACGACGATGCA NO: 14 GCTGGGGCTTG GCGTGGAATGG TTGTCG

The 39.2-cM region is a region that comprises 8 types of markers listed in table 2 below in the order shown in table 2 and is linked to a trait characterized by the improvement of smut resistance.

TABLE 2 Nucleotide Linkage Marker sequence Signal SEQ group name information threshold ID NO: NiF8_17 N826561 GGCCTTGTTTA 1,000 SEQ ID AATGTCACCTA NO: 15 AATTCTAAATT TTACACTCTTT TCATAACATCG AATCTTAAAA N827136 AAACTGAGGGA 1,500 SEQ ID TTACTTTCCAA NO: 16 TTGAAATGTCA TCCACCACAAA CACAAAAGGCA TACTCA N826325 ACACTACACTG 1,000 SEQ ID TGTAGGCAATG NO: 17 AGCAGCTCTGT TGCACAGCAAA GCCAAA N803928 GGATGTGAAGT 1,000 SEQ ID ATGTATGTGTT NO: 18 TTCAGATGGAC CAAGGAAGCTG CATGGG N822568 TACGGTGGTAC 1,000 SEQ ID AAAGCTTAGAT NO: 19 CAATGATCAAG CTACAAAACAC ACAAAGATAGT CAGTAGAAAAA GT N829026 GACGACGAGGT 1,000 SEQ ID GGGCAGCGCCA NO: 20 GTGCGCTACTA CCTTCTTTCTT GCAACT N815300 GTATGGTTATG 1,000 SEQ ID TTGGTACTAAA NO: 21 GGTTTCTGACT ATTGTATTGTA TTGTTGTGTTA TAATGGGTTCA ATG N826906 GGCTGCAATAC 1,000 SEQ ID CTGTTCCTCAT NO: 22 CTCATCTATTC GTGCAAAGTTG CTGGTC

The 19.2-cM region is a region that comprises 10 types of markers listed in table 3 below in the order shown in table 3 and is linked to a trait characterized by the reduction of smut resistance.

TABLE 3 Nucleotide Linkage Marker sequence Signal SEQ group name information threshold ID NO: NiF8_40 N816552 TCGGGTTGGAG 1,500 SEQ ID GCAAGGAAGAA NO: 23 AGGAGCTAGAT TGCTCGGCTGC TGGTGC N827448 ACAGTAGTGCA 1,000 SEQ ID ACTGCGACGAC NO: 24 GATGTGTGGGT ATATGTTCCAT AGCTTG N829378 TTTTGATTGGC   900 SEQ ID CTTGCAGATGT NO: 25 TGCAGCGATGG CACTCGTGGCA AACAGA N829404 AACCATGCTGA 1,000 SEQ ID AAACGTCTTCC NO: 26 GTTTACAGTTT ATGGTATATCC GCTTAAAACTA ACTCGATC N828725 AATCTAAATGA 1,000 SEQ ID CTAATGAGACC NO: 27 GTGAGAGCTGC TTAGCTTAATG GTGCATCCCTT TTTAAACT N812680 AAGAACACTGC 1,500 SEQ ID TAAGGATGGTC NO: 28 ACAATTTGGAA ACTGAAGTTTT ATCTCTGGTTC GGT N811688 AAGCTGCATCT 1,000 SEQ ID GATTCTCATCC NO: 29 AAACCTGCTCT GCTCATTATCA TTACTTCGT N819703 CCAACCAACAG 1,500 SEQ ID CAAGAACACCA NO: 30 AGACGCACATA ATGAGGCCCAT GAAGTA N815648 TTTACACCAGT 1,000 SEQ ID GAACTGACAAA NO: 31 AAATCGAAGTG GTGCGGTACAT AAGAACATTTA CATCCAACT N821999 GACCAATCTAG 1,000 SEQ ID GAAAAACAATT NO: 32 GCACAAATGAC TACATTTATTA TGGCAAATCAA TTTTCTTCAGT CATTGTA

The 32.0-cM region is a region that comprises 19 types of markers listed in table 4 below in the order shown in table 4 and is linked to a trait characterized by the improvement of smut resistance.

TABLE 4 Nucleotide Linkage Marker sequence Signal SEQ group name information threshold ID NO: Ni9_1 N915070 ATAGTCTACCT 1,000 SEQ ID ATACTGGTGCC NO: 33 ACAAGTCAACA AGTGATGGCAA TACCCATTCAA ATT N915209 TGGCAATACCC 1,000 SEQ ID ATTCAAATTGC NO: 34 GTCAAATGTGA ATAAATGGAGG TAGATGACTAA CACCTTTGTTT CAAAA N916186 CTGCAATACAA 1,000 SEQ ID TGCGGTGGAAG NO: 35 CGGATTGGTGG AAGGCATGCAT GCATCA N902342 CCAAATACCTA   900 SEQ ID AGTGCACTTTT NO: 36 TTCTGAGGCCA AATACCTAGGT TCGAAAGATTC GT N919949 CCGCCTCAAAA 1,000 SEQ ID GGAAGTAACAC NO: 37 AGGAACATGAT CATACGGAGTA GTACTAT N920597 CTTGCCGGCCG 1,500 SEQ ID GGACCCTGCTG NO: 38 GCACGATCAAG CGACTACAGTA CAATGC N916081 CAAAGAAAGCA 4,000 SEQ ID CATTACCGCGT NO: 39 ATGTTACCAAC TTCCTATGTTG ACTATCCAAAT ACTG N902047 GGATTGGTCTA 1,500 SEQ ID GTACAATCTTT NO: 40 ATTGAAGACGA AAGATTTATGC ATGGTGATTAG TTGAGCCTGT N916874 CAAATATGACG 1,000 SEQ ID ATGGAAATATA NO: 41 TAGTACTATTA ATAAGACATAA CTTGCAGCATA TATTAATTTCA TAGGATAAG N918161 CTAGTTAGAGC 1,000 SEQ ID ATCTCCAAGCG NO: 42 TACTCAGAAGA GTCGCCCAATC TAGCAA N918536 CAGAGAAACTG   900 SEQ ID GGAACGAAACA NO: 43 GGACAATACAT CTGTACGTTTG GCTTGT N901676 TCCCTGTACTG 1,000 SEQ ID TATGGTCGCCA NO: 44 CAAATGCATAT TGATAGACATG TTTATGATGTA GAATTTGATGT TTACA N919743 AAATCAATAAA 1,000 SEQ ID GAAAGGCACGC NO: 45 TGAAAATAAGA TGGTCTGATCG AGCTCCTGTGT TTAGTACAA N901176 ATTCCAATGAA 1,500 SEQ ID CTAAGGGTAAG NO: 46 TAGAGATTATT ATATATAAATC AATGATACACA AACTGATCAAT CAACTAA N916035 GCCTTCTTGAT 1,500 SEQ ID CTCTCAGACTA NO: 47 AGAACATAGGC CCAGAGTGAGG GGAAAC N921010 CGTTCGCTTGA 1,500 SEQ ID GCTTATTAGAT NO: 48 AAAATCAATCA GCAATAAAATA ATATTTTTTTC TAATAAAAATC AGCA N915635 TTTATCAGCTT 4,000 SEQ ID CGGAAATCAGC NO: 49 TTGAGCTGACG AAGACATCAAT CTTCTACATCA GAT N901348 ACATGTATGTG 1,500 SEQ ID CAAAATATCTT NO: 50 GAGACCCTCTG CTTTAACATGC ATGTCCTTCAC ATGT N920207 CAGCTCTGTCA 1,500 SEQ ID TTGCCGCCAAA NO: 51 CACATATGCGC CTTCATGCCCT TCTCCC

The 39.5-cM region is a region that comprises 11 types of markers listed in table 5 below in the order shown in table 5 and is linked to a trait characterized by the reduction of smut resistance.

TABLE 5 Nucleotide Linkage Marker sequence Signal SEQ group name information threshold ID NO: Ni9_13 N914284 AGCCATCCCGC 1,000 SEQ ID AGAGGCTCTTG NO: 52 ATGTCCTTTGA GCTGTCCTAAA ACCACT N901453 CTATGTGTTGG 1,000 SEQ ID GCTTATATGTG NO: 53 ATGCATCTTTC CTTTTGAATTC AGGGTAGTGCT GATA N900044 GTGCTGATACG 1,000 SEQ ID CCACCAGCCGA NO: 54 AACAAATGGTG ATAGCTCTAGC GCACAG N919839 AAATCCTGAAG 1,500 SEQ ID GCCGAAGCCCG NO: 55 TAGACATGTTC ACCCTAGCAAA CAAAGG N901567 GCATCGGCTGG 1,500 SEQ ID TGCTGGTAGGG NO: 56 ATAAACCTCTG CTCCGCTTGAT ATTTTT N911103 TTCGCTTGAGT   800 SEQ ID TTTATCAGCAG NO: 57 AATTAACAGTT ATATAGCGGTG TTTTTTCTCTC ACACTAAATCA GTAAA N918508 CTTGCCTACTT 1,500 SEQ ID CTTGCATAGAT GCTTAGTTTAC NO: 58 ATTTTACCTGA AATTTATTAAT ATCGATCACTA CAAAT N918344 GAACAAGGAGC 1,000 SEQ ID ATCCATATATG NO: 59 TATGGCACTTT GACATTGTTGG CTATGTCTAGC TT N919696 GGAAAAGCAAG 1,000 SEQ ID CAGCTCGTGTA NO: 60 GCAATAGTTGG CATTGGCAACA GACGCC N916172 GGTAAAATTAT 1,500 SEQ ID GCAAGTTCCCA NO: 61 CGAAATTTGGC ATATGAAAGTG CCCTTAAAAAT TAAGGTTT N916129 GAGCTTTTATT 1,500 SEQ ID TATGCTAACCT NO: 62 GTAACAATAAA TTGTCTTTGAG CATGGTTTGTT TGATGATCTCA ATGACCG

The 53.4-cM region is a region that comprises 10 types of markers listed in table 6 below in the order shown in table 6 and is linked to a trait characterized by the reduction of smut resistance.

TABLE 6 Nucleotide Linkage Marker sequence Signal SEQ group name information threshold ID NO: Ni9_14_1 N901178 ATCTACACAAC 1,000 SEQ ID AAATCCACTGT NO: 63 ATTAGACGATT GTTATCAAATG ATCTTCCAGCA AATTGACATAA TATGACATT N918761 AGAACAGGGCC 1,500 SEQ ID ATCGTTGTTAG NO: 64 CGTGCGTGCTG TAAGTTTGATT TAATTTAAAAA AAATACGTATA N913735 ACGTACAAATG 1,000 SEQ ID TTTGGGATGGC NO: 65 AGAGGACATGT AGTACAGGGTT GATTCTTTTCA ATA N900663 GCACCTCGCTC 1,000 SEQ ID CTCCTTATCAA NO: 66 GTTTCGATTTC TGGATTTGCTG CTCTTG N918363 AAGGCGAACAA 1,000 SEQ ID ATGATTCCCCT NO: 67 CAGTGACCTGA ACGTAATAGTA AAATGATACAC ACT N918213 TCGCATGTCAG 1,500 SEQ ID GGCTGACAAAT NO: 68 GGCTAAAACCA GACGGAAGATA GACGGA N900568 AACATCAGCTT 1,000 SEQ ID AGTCTTTAGAG NO: 69 GTTATACCTGC TGTGCTATTTT TTTTACTTAGT GTACACCATTC CTGA N912523 CCTTAATCACG 1,500 SEQ ID CTTGTGAAATA NO: 70 TCACTCAAACC AACAATATCAA TACCACCATTA ATTATGCTTGT GAAATATGC N900344 TTAAAGACTGA 1,500 SEQ ID AAGAAACAATT NO: 71 ATTGAATTAAA GAACAACTAGA TAGAGAGCACT GGACTGAATGG TTGCAGA N900802 ATCCCATCACA 1,500 SEQ ID AAGGAAAGAAT NO: 72 TGCACAAACAA TGACGTGGTAC CTTTAAAAGAT AGAGAATGGAA TAGA

The 38.0-cM region is a region that comprises 13 types of markers listed in table 7 below in the order shown in table 7 and is linked to a trait characterized by the improvement of smut resistance.

TABLE 7 Nucleotide Linkage Marker sequence Signal SEQ group name information threshold ID NO: Ni9_14_2 N901524 AAGCAACAGAT 1,000 SEQ ID GACTAGAAGTA NO: 73 CAGTGCAGGAG ACTCCAACACT TTACTATATTA GTAGAAGA N901163 TCTTCAGTTCA 1,000 SEQ ID TATCTATCATC NO: 74 TATCCGTCGCT CGTTTCATGAG ACAGATCAAAT AAGCAGAT N911063 TTCGAGAATGA 1,000 SEQ ID GCGCATTAGCA NO: 75 CAAGGTTTAAT TTCATTAATCA CTTTAGGTATC TAGTTAGGTGT GTGT N914692 CGCCCACCAAT 1,500 SEQ ID GCATTACCCAA NO: 76 TGGGGTACCCG ATGCCGCCCCA TTCGCA N911405 GTGCAGGGTAC 1,000 SEQ ID CCGTCAATGGG NO: 77 CTACGGCTATG GCCGCCCACCA ATGCAT N913383 AAGATAAATTT 1,000 SEQ ID ACAAGCAAAAT NO: 78 TAGAATGTCAA ATACCACAAAT ATTGAGAGCTG TGCCTGACAAT TGAGGAGA N914112 AGCTGTGCCTG 1,000 SEQ ID ACAATTGAGAG NO: 79 TGAACAGAGTA CATTTCATACT GCCCAG N915180 TCCGGAGATTA 1,000 SEQ ID CAACGTCTTCA NO: 80 GTGACGAGAAC CCGAACAGCTG CTCGGT N901160 CCCCTGACACG 1,500 SEQ ID ATATTTATTTG NO: 81 CCAGAATTTAT GAATTACAGCC GCATTTCGTTG TGT N916293 TTGGCAATCAT 1,000 SEQ ID CGACTAATTAG NO: 82 GTGTAAAAGAT TCGTCTTGTTA TTTTCTACCAA ATTATGAAATT TA N916263 TATAGGGCCAG 1,000 SEQ ID ATAAACCATGA NO: 83 TAATCATAGGA TATTTGCAGAA ATCTTAAATTT CTGAGATTGCC AACAGAAGA N917579 TATGGATCTTC 1,000 SEQ ID CAGTTGATTAC NO: 84 TGTTCTTTCGC TCCGCTTTTTG CTTTTTTACTC GTGA N918080 TACTCGTGAGG 1,000 SEQ ID GTCCATCTATG NO: 85 ACCTATCCTGT GTTCTTTACTA GCGAAA

In addition, in tables 1 to 7, “Linkage group” represents the number given to each group among a plurality of linkage groups specified by QTL analysis. In tables 1 to 7, “Marker name” represents the name given to each marker originally obtained in the present invention. In tables 1 to 7, “Signal threshold” represents a threshold used for determination of the presence or absence of a marker.

In addition, the peak contained in the 18.7-cM region is present in a region sandwiched between a marker (N804607) consisting of the nucleotide sequence shown in SEQ ID NO: 5 and a marker (N815502) consisting of the nucleotide sequence shown in SEQ ID NO: 9. The peak contained in the 39.2-cM region is present in a region sandwiched between a marker (N803928) consisting of the nucleotide sequence shown in SEQ ID NO: 18 and a marker (N826906) consisting of the nucleotide sequence shown in SEQ ID NO: 22. The peak contained in the 19.2-cM region is present in a region sandwiched between a marker (N829378) consisting of the nucleotide sequence shown in SEQ ID NO: 25 and a marker (N821999) consisting of the nucleotide sequence shown in SEQ ID NO: 32. The peak contained in the 32.0-cM region is present in a region sandwiched between a marker (N915070) consisting of the nucleotide sequence shown in SEQ ID NO: 33 and a marker (N918161) consisting of the nucleotide sequence shown in SEQ ID NO: 42. The peak contained in the 39.5-cM region is present in a region sandwiched between a marker (N911103) consisting of the nucleotide sequence shown in SEQ ID NO: 57 and a marker (N918344) consisting of the nucleotide sequence shown in SEQ ID NO: 59. The peak contained in the 53.4-cM region is present in a region sandwiched between a marker (N918761) consisting of the nucleotide sequence shown in SEQ ID NO: 64 and a marker (N900663) consisting of the nucleotide sequence shown in SEQ ID NO: 66. The peak contained in the 38.0-cM region is present in a region sandwiched between a marker (N901524) consisting of the nucleotide sequence shown in SEQ ID NO: 73 and a marker (N915180) consisting of the nucleotide sequence shown in SEQ ID NO: 80.

A continuous nucleic acid region existing in any of 7 regions containing markers shown in tables 1 to 7 can be used as a marker associated with resistance to sugarcane smut. The term “nucleic acid region” used herein refers to a region having a nucleotide sequence having 95% or less, preferably 90% or less, more preferably 80% or less, and most preferably 70% or less identity to a different region present on a sugarcane chromosome. If the identity of a nucleic acid region serving as a marker associated with resistance to sugarcane smut to a different region falls within the above range, the nucleic acid region can be specifically detected according to a standard method. The identity value described herein can be calculated using default parameters and BLAST® or a similar algorithm.

In addition, the base length of a nucleic acid region serving as a marker associated with resistance to sugarcane smut can be at least 8 bases, preferably 15 bases or more, more preferably 20 bases or more, and most preferably 30 bases. If the base length of a nucleic acid region serving as a marker associated with resistance to sugarcane smut falls within the above range, the nucleic acid region can be specifically detected according to a standard method.

In particular, among the 14 types of markers contained in the 18.7-cM region, a marker associated with resistance to sugarcane smut is preferably designated as existing in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 5 and the nucleotide sequence shown in SEQ ID NO: 9. This is because the above peak is present in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 5 and the nucleotide sequence shown in SEQ ID NO: 9. In addition, among the 8 types of markers contained in the 39.2-cM region, a marker associated with resistance to sugarcane smut is preferably designated as existing in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 18 and the nucleotide sequence shown in SEQ ID NO: 22. This is because the above peak is present in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 18 and the nucleotide sequence shown in SEQ ID NO: 22. Further, among the 10 types of markers contained in the 19.2-cM region, a marker associated with resistance to sugarcane smut is preferably designated as existing in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 25 and the nucleotide sequence shown in SEQ ID NO: 32. This is because the above peak is present in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 25 and the nucleotide sequence shown in SEQ ID NO: 30. Furthermore, among the 19 types of markers contained in the 32.0-cM region, a marker associated with resistance to sugarcane smut is preferably designated as existing in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 33 and the nucleotide sequence shown in SEQ ID NO: 42. This is because the above peak is present in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 33 and the nucleotide sequence shown in SEQ ID NO: 42. Moreover, among the 11 types of markers contained in the 39.5-cM region, a marker associated with resistance to sugarcane smut is preferably designated as existing in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 57 and the nucleotide sequence shown in SEQ ID NO: 59. This is because the above peak is present in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 57 and the nucleotide sequence shown in SEQ ID NO: 59. Among the 10 types of markers contained in the 53.4-cM region, a marker associated with resistance to sugarcane smut is preferably designated as existing in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 64 and the nucleotide sequence shown in SEQ ID NO: 66. This is because the above peak is present in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 64 and the nucleotide sequence shown in SEQ ID NO: 66. Among the 13 types of markers contained in the 38.0-cM region, a marker associated with resistance to sugarcane smut is preferably designated as existing in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 73 and the nucleotide sequence shown in SEQ ID NO: 80. This is because the above peak is present in the region sandwiched between the nucleotide sequence shown in SEQ ID NO: 73 and the nucleotide sequence shown in SEQ ID NO: 80.

In addition, a nucleic acid region containing a single marker selected from among the 85 types of markers shown in tables 1 to 7 can be used as a marker associated with resistance to sugarcane smut. For example, it is preferable to use, as a marker associated with resistance to sugarcane smut, a nucleic acid region containing a marker (N802870) consisting of the nucleotide sequence shown in SEQ ID NO: 6 located closest to the peak position in the 18.7-cM region, a nucleic acid region containing a marker (N826906) consisting of the nucleotide sequence shown in SEQ ID NO: 22 located closest to the peak position in the 39.2-cM region, a nucleic acid region containing a marker (N821999) consisting of the nucleotide sequence shown in SEQ ID NO: 32 located closest to the peak position in the 19.2-cM region, a nucleic acid region containing a marker (N916186) consisting of the nucleotide sequence shown in SEQ ID NO: 35 located closest to the peak position in the 32.0-cM region, a nucleic acid region containing a marker (N918508) consisting of the nucleotide sequence shown in SEQ ID NO: 58 located closest to the peak position in the 39.5-cM region, a nucleic acid region containing a marker (N913735) consisting of the nucleotide sequence shown in SEQ ID NO: 65 located closest to the peak position in the 53.4-cM region, or a nucleic acid region containing a marker (N901163) consisting of the nucleotide sequence shown in SEQ ID NO: 74 located closest to the peak position in the 38.0-cM region. In such case, the nucleotide sequence of a nucleic acid region containing the marker can be specified by flanking sequence analysis such as inverse PCR analysis using primers designed based on the nucleotide sequence of such marker.

Further, as a marker associated with resistance to sugarcane smut, any of the above 85 types of markers can be directly used. Specifically, one or more type(s) of markers selected from among the 85 types of such markers can be directly used as a marker associated with resistance to sugarcane smut. For example, it is preferable to use, as a marker associated with resistance to sugarcane smut, a marker (N802870) consisting of the nucleotide sequence shown in SEQ ID NO: 6 located closest to the peak position in the 18.7-cM region, a marker (N826906) consisting of the nucleotide sequence shown in SEQ ID NO: 22 located closest to the peak position in the 39.2-cM region, a marker (N821999) consisting of the nucleotide sequence shown in SEQ ID NO: 32 located closest to the peak position in the 19.2-cM region, a marker (N916186) consisting of the nucleotide sequence shown in SEQ ID NO: 35 located closest to the peak position in the 32.0-cM region, a marker (N918508) consisting of the nucleotide sequence shown in SEQ ID NO: 58 located closest to the peak position in the 39.5-cM region, a marker (N913735) consisting of the nucleotide sequence shown in SEQ ID NO: 65 located closest to the peak position in the 53.4-cM region, or a marker (N901163) consisting of the nucleotide sequence shown in SEQ ID NO: 74 located closest to the peak position in the 38.0-cM region.

<Sugarcane Marker Identification>

As described above, markers associated with resistance to sugarcane smut were identified from among 3004 markers and 4569 markers originally obtained from sugarcane chromosomes in the present invention. The 3004 markers and the 4569 markers are described below. Upon identification of these markers, a DNA microarray can be used according to the method disclosed in JP Patent Application No. 2009-283430.

Specifically, the 3004 markers and the 4569 markers originally obtained from sugarcane chromosomes are used with a DNA microarray having probes designed by the method disclosed in JP Patent Application No. 2009-283430. The method for designing probes as shown in FIG. 1 is described below. First, genomic DNA is extracted from sugarcane (step 1a). Next, the extracted genomic DNA is digested with a single or a plurality of restriction enzyme(s) (step 1b). In addition, in the example shown in FIG. 1, 2 types of restriction enzymes illustrated as restriction enzymes A and B are used (in the order of A first and then B) to digest genomic DNA. The restriction enzymes used herein are not particularly limited. However, examples of restriction enzymes that can be used include PstI, EcoRI, HindIII, BstNI, HpaII, and HaeIII. In particular, restriction enzymes can be adequately selected in consideration of the frequency of appearance of recognition sequences such that a genomic DNA fragment having a base length of 20 to 10000 can be obtained when genomic DNA is completely digested. In addition, when a plurality of restriction enzymes are used, it is preferable for a genomic DNA fragment obtained after the use of all restriction enzymes to have a base length of 200 to 6000. Further, when a plurality of restriction enzymes are used, the order in which restriction enzymes are subjected to treatment is not particularly limited. In addition, a plurality of restriction enzymes may be used in an identical reaction system if they are treated under identical conditions (e.g., solution composition and temperature). Specifically, in the example shown in FIG. 1, genomic DNA is digested using restriction enzymes A and B in such order. However, genomic DNA may be digested by simultaneously using restriction enzymes A and B in an identical reaction system. Alternatively, genomic DNA may be digested using restriction enzymes B and A in such order. Further, 3 or more restriction enzymes may be used.

Next, adapters are bound to a genomic DNA fragment subjected to restriction enzyme treatment (step 1c). The adapter used herein is not particularly limited as long as it can be bound to both ends of a genomic DNA fragment obtained by the above restriction enzyme treatment. For example, it is possible to use, as an adapter, an adapter having a single strand complementary to a protruding end (sticky end) formed at each end of genomic DNA by restriction enzyme treatment and a primer binding sequence to which a primer used upon amplification treatment as described in detail below can hybridize. In addition, it is also possible to use, as an adapter, an adapter having a single strand complementary to the above protruding end (sticky end) and a restriction enzyme recognition site that is incorporated into a vector upon cloning.

In addition, when genomic DNA is digested using a plurality of restriction enzymes, a plurality of adapters corresponding to the relevant restriction enzymes can be prepared and used. Specifically, it is possible to use a plurality of adapters having single strands complementary to different protruding ends formed upon digestion of genomic DNA with a plurality of restriction enzymes. Here, a plurality of adapters corresponding to a plurality of restriction enzymes each may have a common primer binding sequence such that a common primer can hybridize to each such adapter. Alternatively, they may have different primer binding sequences such that different primers can separately hybridize thereto.

Further, when genomic DNA is digested using a plurality of restriction enzymes, it is possible to prepare and use, as an adaptor, adapter(s) corresponding to one or a part of restriction enzyme(s) selected from among a plurality of the used restriction enzymes.

Next, a genomic DNA fragment to both ends of which adapters have been added is amplified (step 1d). When an adapter having a primer binding sequence is used, the genomic DNA fragment can be amplified using a primer that can hybridize to the primer binding sequence. Alternatively, a genomic DNA fragment to which an adapter has been added is cloned into a vector using the adapter sequence. The genomic DNA fragment can be amplified using primers that can hybridize to specific regions of the vector. In addition, as an example, PCR can be used for a genomic DNA fragment amplification reaction using primers.

When genomic DNA is digested using a plurality of restriction enzymes and a plurality of adapters corresponding to the relevant restriction enzymes are ligated to genomic DNA fragments, the adapters are ligated to all genomic DNA fragments obtained by treatment with a plurality of restriction enzymes. In this case, all the obtained genomic DNA fragments can be amplified by carrying out a nucleic acid amplification reaction using primer binding sequences contained in adapters.

Alternatively, when genomic DNA is digested using a plurality of restriction enzymes, followed by ligation of adapter(s) corresponding to one or a part of restriction enzyme(s) selected from among a plurality of the used restriction enzymes to genomic DNA fragments, among the obtained genomic DNA fragments, a genomic DNA fragment to both ends of which the selected restriction enzyme recognition sequences have been ligated can be exclusively amplified.

Next, the nucleotide sequence of the amplified genomic DNA fragment is determined (step 1e). Then, one or more region, which has a base length shorter than the base length of the genomic DNA fragment and corresponds to at least a partial region of the genomic DNA fragment, is specified. Sugarcane probes are designed using at least one of the thus specified regions (step 1f). A method for determining the nucleotide sequence of a genomic DNA fragment is not particularly limited. A conventionally known method using a DNA sequencer applied to the Sanger method or the like can be used. For example, a region to be designed herein has a 20- to 100-base length, preferably a 30- to 90-base length, and more preferably a 50- to 75-base length as described above.

A DNA microarray can be produced by designing many probes using genomic DNA extracted from sugarcane as described above and synthesizing an oligonucleotide having a desired nucleotide sequence on a support based on the nucleotide sequence of the designed probe. With the use of a DNA microarray prepared as described above, the 3004 markers and the 4569 markers, including the above 85 types of markers associated with resistance to sugarcane smut shown in SEQ ID NOS: 1 to 85, can be identified.

More specifically, the present inventors obtained signal data of known sugarcane varieties (NiF8 and Ni9) and a progeny line (line 191) obtained by crossing the varieties with the use of the DNA microarray described above. Then, genotype data were obtained based on the obtained signal data. Based on the obtained genotype data, chromosomal marker position information was obtained by calculation using the gene distance function (Kosambi) and the AntMap genetic map creation software (Iwata H, Ninomiya S (2006) AntMap: constructing genetic linkage maps using an ant colony optimization algorithm, Breed Sci 56: 371-378). Further, a genetic map datasheet was created based on the obtained marker position information using Mapmaker/EXP ver. 3.0 (A Whitehead Institute for Biomedical Research Technical Report, Third Edition, January, 1993). As a result, the 3004 markers and the 4569 markers, including the aforementioned 85 types of markers associated with resistance to sugarcane smut shown in SEQ ID NOS: 1 to 85, were identified.

<Use of Markers Associated with Resistance to Sugarcane Smut>

The use of markers associated with resistance to sugarcane smut makes it possible to determine whether a sugarcane progeny line or the like, which has a phenotype exhibiting unknown smut resistance, is a line having a phenotype showing the improvement of smut resistance. The expression “the use of markers associated with resistance to sugarcane smut” used herein indicates the use of a DNA microarray having probes corresponding to markers associated with resistance to sugarcane smut in one embodiment. The expression “probes corresponding to markers associated with resistance to sugarcane smut” indicates oligonucleotides that can specifically hybridize under stringent conditions to markers associated with resistance to sugarcane smut defined as above. For instance, such oligonucleotides can be designed as partial or whole regions with base lengths of at least 10 continuous bases, continuous bases, 20 continuous bases, 25 continuous bases, 30 continuous bases, 35 continuous bases, 40 continuous bases, 45 continuous bases, or 50 or more continuous bases of the nucleotide sequences or complementary strands thereof of markers associated with resistance to sugarcane smut defined as above. In addition, a DNA microarray having such probes may be any type of microarray, such as a microarray having a planar substrate comprising glass, silicone, or the like as a carrier, a bead array comprising microbeads as carriers, or a three-dimensional microarray having an inner wall comprising hollow fibers to which probes are fixed.

The use of a DNA microarray prepared as described above makes it possible to determine whether a sugarcane line such as a progeny line or the like, which has a phenotype exhibiting unknown smut resistance, is a line having a phenotype showing the improvement of smut resistance. In addition, in the case of a method other than the above method involving the use of a DNA microarray, it is also possible to determine whether a sugarcane line, which has a phenotype exhibiting unknown smut resistance, is a line having a trait characterized by the improvement of smut resistance by detecting the above markers associated with resistance to sugarcane smut by a conventionally known method.

The method involving the use of a DNA microarray is described in more detail. As shown in FIG. 2, first, genomic DNA is extracted from a sugarcane sample. In this case, a sugarcane sample is a sugarcane line such as a sugarcane progeny line, which has a phenotype exhibiting unknown smut resistance, and/or a sugarcane line used as a parent for producing a progeny line, and thus which can be used as a subject to be determined whether to have a trait characterized by the improvement of smut resistance or not. In addition, it is also possible to evaluate smut resistance in a sample plant which is a non-sugarcane plant such as a graminaceous plant (e.g., Sorghum or Erianthus).

Next, a plurality of genomic DNA fragments are prepared by digesting the extracted genomic DNA with restriction enzymes used for preparing the DNA microarray. Then, the obtained genomic DNA fragments are ligated to adapters used for preparation of the DNA microarray. Subsequently, the genomic DNA fragments, to both ends of which adapters have been added, are amplified using primers employed for preparation of the DNA microarray. Accordingly, sugarcane-sample-derived genomic DNA fragments corresponding to the genomic DNA fragments amplified in step 1d upon preparation of the DNA microarray can be amplified.

In this step, among the genomic DNA fragments to which adapters have been added, specific genomic DNA fragments may be selectively amplified. For instance, in a case in which a plurality of adapters corresponding to a plurality of restriction enzymes are used, genomic DNA fragments to which specific adapters have been added can be selectively amplified. In addition, when genomic DNA is digested with a plurality of restriction enzymes, genomic DNA fragments to which adapters have been added can be selectively amplified by adding adapters only to genomic DNA fragments that have protruding ends corresponding to specific restriction enzymes among the obtained genomic DNA fragments. Thus, specific DNA fragment concentration can be increased by selectively amplifying the specific genomic DNA fragments.

Thereafter, amplified genomic DNA fragments are labeled. Any conventionally known substance may be used as a labeling substance. Examples of a labeling substance that can be used include fluorescent molecules, dye molecules, and radioactive molecules. In addition, this step can be omitted using a labeled nucleotide in the step of amplifying genomic DNA fragments. This is because when genomic DNA fragments are amplified using a labeled nucleotide in the amplification step, amplified DNA fragments can be labeled.

Next, labeled genomic DNA fragments are allowed to come into contact with the DNA microarray under certain conditions such that probes fixed to the DNA microarray hybridize to the labeled genomic DNA fragments. At such time, preferably, highly stringent conditions are provided for hybridization. Under highly stringent conditions, it becomes possible to determine with high accuracy whether or not markers associated with resistance to sugarcane smut are present in a sugarcane sample. In addition, stringent conditions can be adjusted based on reaction temperature and salt concentration. That is, an increase in temperature or a decrease in salt concentration results in more stringent conditions. For example, when a probe having a length of 50 to 75 bases is used, the following more stringent conditions can be provided as hybridization conditions: 40 degrees C. to 44 degrees C.; 0.21 SDS; and 6×SSC.

In addition, hybridization between labeled genomic DNA fragments and probes can be confirmed by detecting a labeling substance. Specifically, after the above hybridization reaction of labeled genomic DNA fragments and probes, unreacted genomic DNA fragments and the like are washed, and the labeling substance bound to each genomic DNA fragment specifically hybridizing to a probe is observed. For instance, in a case in which the labeling substance is a fluorescent material, the fluorescence wavelength is detected. In a case in which the labeling substance is a dye molecule, the dye wavelength is detected. More specifically, apparatuses such as fluorescent detectors and image analyzers used for conventional DNA microarray analysis can be used.

As described above, it is possible to determine whether or not a sugarcane sample has the above markers associated with resistance to sugarcane smut with the use of the DNA microarray. Here, as described above, as the marker associated with resistance to sugarcane smut, a marker linked to a trait characterized by the improvement of smut resistance and a marker linked to a trait characterized by the reduction of smut resistance are provided. Markers associated with resistance to sugarcane smut designed based on the three aforementioned regions identified in tables 2, 4, and 7 are linked to a trait characterized by the improvement of smut resistance. Meanwhile, markers associated with resistance to sugarcane smut designed based on the four aforementioned regions identified in tables 1, 3, 5, and 6 are linked to a trait characterized by the reduction of smut resistance.

Therefore, if any one of the markers associated with resistance to sugarcane smut designed based on the three aforementioned regions identified in tables 2, 4, and 7 is present in a sugarcane sample, it is possible to determine that the sample is of a variety with improved smut resistance. Further, if any one of the markers associated with resistance to sugarcane smut designed based on the four aforementioned regions identified in tables 1, 3, 5, and 6 is absent in a sugarcane sample, it is possible to determine that the sample is of a variety with improved smut resistance. Preferably, if any one of the markers associated with resistance to sugarcane smut designed based on the three aforementioned regions identified in tables 2, 4, and 7 is present in a sugarcane sample, and if any one of the markers associated with resistance to sugarcane smut designed based on the four aforementioned regions identified in tables 1, 3, 5, and 6 is absent in the sugarcane sample, it is possible to determine with high accuracy that the sample is of a variety with improved smut resistance.

In particular, according to the method described above, it is not necessary to cultivate sugarcane samples to such an extent that determination using an actual smut resistance test becomes possible. For instance, seeds of a progeny line or a young seedling obtained as a result of germination of such seeds can be used. Therefore, the area of a field used for cultivation of sugarcane samples and other factors such as cost of cultivation can be significantly reduced with the use of the markers associated with resistance to sugarcane smut. In addition, the use of markers associated with resistance to sugarcane smut makes it possible to reduce the cost of facilities such as a large-scale special-purpose greenhouse, a special-purpose field, or isolation facility from an external environment, without the need to actually cause infection with a causative microorganism of smut (Ustilago scitaminea).

In particular, when a novel sugarcane variety is created, it is preferable to produce several tens of thousands of seedlings via crossing and then to identify a novel sugarcane variety using markers associated with resistance to sugarcane smut prior to or instead of seedling selection. The use of such markers associated with resistance to sugarcane smut makes it possible to significantly reduce the number of excellent lines that need to be cultivated in an actual field. This allows drastic reduction of time-consuming efforts and the cost required to create a novel sugarcane variety.

Alternatively, upon creation of a new sugarcane variety, firstly, it may be determined whether or not a marker associated with resistance to sugarcane smut is present in a parent variety used for crossing, thereby allowing selection of a parent variety with excellent smut resistance. It can be expected that a progeny line with excellent smut resistance will be obtained with high frequency by creating a parent variety with excellent smut resistance on a priority basis. The use of such marker(s) associated with resistance to sugarcane smut makes it possible to significantly reduce the number of excellent lines that need to be cultivated. This allows drastic reduction of time-consuming efforts and the cost required to create a novel sugarcane variety.

EXAMPLES

The present invention is hereafter described in greater detail with reference to the following examples, although the technical scope of the present invention is not limited thereto.

1. Production of DNA Microarray Probes

(1) Materials

The following varieties were used: sugarcane varieties: NiF8, Ni9, US56-15-8, POJ2878, Q165, R570, Co290 and B3439; closely-related sugarcane wild-type varieties: Glagah Kloet, Chunee, Natal Uba, and Robustum 9; and Erianthus varieties: IJ76-349 and JW630.

(2) Restriction Enzyme Treatment

Genomic DNA was extracted from each of the above sugarcane varieties, closely-related sugarcane wild-type varieties, and Erianthus varieties using DNeasy Plant Mini Kits (Qiagen). Genomic DNAs (750 ng each) were treated with a PstI restriction enzyme (NEB; 25 units) at 37 degrees C. for 2 hours. A BstNI restriction enzyme (NEB; 25 units) was added thereto, followed by treatment at 60 degrees C. for 2 hours.

(3) Adapter Ligation

PstI sequence adapters (5′-CACGATGGATCCAGTGCA-3′ (SEQ ID NO: 86) and 5′-CTGGATCCATCGTGCA-3′ (SEQ ID NO: 87)) and T4 DNA Ligase (NEB; 800 units) were added to the genomic DNA fragments treated in (2) (120 ng each), and the obtained mixtures were subjected to treatment at 16 degrees C. overnight. Thus, the adapters were selectively added to genomic DNA fragments having PstI recognition sequences at both ends thereof among the genomic DNA fragments treated in (2).

(4) PCR Amplification

A PstI sequence adapter recognition primer (5′-GATGGATCCAGTGCAG-3′ (SEQ ID NO: 88)) and Taq polymerase (TAKARA; PrimeSTAR; 1.25 units) were added to the genomic DNA fragment (15 ng) having the adaptors obtained in (3). Then, the genomic DNA fragment was amplified by PCR (treatment at 98 degrees C. for 10 seconds, 55 degrees C. for 15 seconds, 72 degrees C. for 1 minute for 30 cycles, and then at 72 degrees C. for 3 minutes, followed by storage at 4 degrees C.).

(5) Genome Sequence Acquisition

The nucleotide sequence of the genomic DNA fragment subjected to PCR amplification in (4) was determined by the Sanger method. In addition, information on a nucleotide sequence sandwiched between PstI recognition sequences was obtained based on the total sorghum genome sequence information contained in the genome database (Gramene).

(6) Probe Design and DNA Microarray Production

50- to 75-bp probes were designed based on the genome sequence information in (5). Based on the nucleotide sequence information of the designed probes, a DNA microarray having the probes was produced.

2. Acquisition of Signal Data Using a DNA Microarray

(1) Materials

Sugarcane varieties/lines (NiF8 and Ni9) and the progeny line (line 191) were used.

(2) Restriction Enzyme Treatment

Genomic DNAs were extracted from NiF8, Ni9, and the progeny line (line 191) using DNeasy Plant Mini Kits (Qiagen). Genomic DNAs (750 ng each) were treated with a PstI restriction enzyme (NEB; 25 units) at 37 degrees C. for 2 hours. Then, a BstNI restriction enzyme (NEB; 25 units) was added thereto, followed by treatment at 60 degrees C. for 2 hours.

(3) Adapter Ligation

PstI sequence adapters (5′-CACGATGGATCCAGTGCA-3′ (SEQ ID NO: 86) and 5′-CTGGATCCATCGTGCA-3′ (SEQ ID NO: 87)) and T4 DNA Ligase (NEB; 800 units) were added to the genomic DNA fragments treated in (2) (120 ng each), and the obtained mixtures were treated at 16 degrees C. overnight. Thus, the adaptors were selectively added to a genomic DNA fragment having PstI recognition sequences at both ends thereof among the genomic DNA fragments treated in (2).

(4) PCR Amplification

A PstI sequence adapter recognition primer (5′-GATGGATCCAGTGCAG-3′ (SEQ ID NO: 88)) and Taq polymerase (TAKARA; PrimeSTAR; 1.25 units) were added to the genomic DNA fragment (15 ng) having the adapters obtained in (3). Then, the genomic DNA fragment was amplified by PCR (treatment at 98 degrees C. for 10 seconds, 55 degrees C. for 15 seconds, 72 degrees C. for 1 minute for 30 cycles, and then 72 degrees C. for 3 minutes, followed by storage at 4 degrees C.).

(5) Labeling

The PCR amplification fragment obtained in (4) above was purified with a column (Qiagen). Cy3-labeled 9mers (TriLink; 1 O.D.) was added thereto. The resultant was treated at 98 degrees C. for 10 minutes and allowed to stand still on ice for 10 minutes. Then, Klenow (NEB; 100 units) was added thereto, followed by treatment at 37 degrees C. for 2 hours. Thereafter, a labeled sample was prepared by ethanol precipitation.

(6) Hybridization/Signal Detection

The labeled sample obtained in (5) was subjected to hybridization using the DNA microarray prepared in 1 above in accordance with the NimbleGen Array User's Guide. Signals from the label were detected.

3. Identification of QTL for Sugarcane Smut Resistance and Development of Markers

(1) Creation of Genetic Map Datasheet

Genotype data of possible 3004 markers and 4569 markers were obtained based on the signal data detected in 2 above of the NiF8 and Ni9 sugarcane varieties and the progeny line (line 191). Based on the obtained genotype data, chromosomal marker position information was obtained by calculation using the gene distance function (Kosambi) and the AntMap genetic map creation software (Iwata H, Ninomiya S (2006) AntMap: constructing genetic linkage maps using an ant colony optimization algorithm, Breed Sci 56: 371-378). Further, a genetic map datasheet was created based on the obtained marker position information using Mapmaker/EXP ver. 3.0 (A Whitehead Institute for Biomedical Research Technical Report, Third Edition, January, 1993).

(2) Acquisition of Smut Resistance Data

From October 26 to 28, 2009, stalks of NiF8, Ni9, and the 191 hybrid progeny line were harvested. They were subjected to treatment for stimulating germination at room temperature and high humidity for 2 to 3 days, followed by wound inoculation with smut spores. For wound inoculation, wounds were made on both sides of buds (6 wounds in total; approximately 4.0 mm in depth), and then a spore suspension (10⁷ to 10⁸ spores/ml) was applied to the wounds using a brush. Smut spores in the spore suspension were collected from smut whips of Ni9 stocks naturally infected with smut, which were cultivated in Okinawa in 2009. Seedlings subjected to wound inoculation were cultivated for 2 to 3 days at room temperature and high humidity and planted in nursery boxes from Oct. 30 to Nov. 1, 2009 (40 buds/box, 2 boxes/line). The planted seedlings were cultivated at high humidity in a greenhouse until Sep. 2, 2010. The degree of the development of smut was investigated by counting, as the number of affected seedlings, the number of seedlings showing a symptom of smut, which is the outgrowth of a smut whip from the apex of a stalk. After the count of the affected seedlings, the plant bodies of affected seedlings were harvested at the ground level so that they could be removed. The number of seedlings affected with smut was investigated on June 23, July 21, August 18, and Sep. 2, 2010 for a total of four instances. The incidence of smut was calculated as a percentage of the number of germinating stocks (excluding stocks killed by non-smut causes) accounted for by the number of affected stocks. FIGS. 3, 4, 5, and 6 show the study results of Jun. 23, 2010, the study results of Jul. 21, 2010, the study results of Aug. 18, 2010, and the study results of Sep. 2, 2010, respectively.

(3) Quantitative Trait (Quantitative Trait Loci: QTL) Analysis

Based on the genetic map datasheet obtained in (1) above and the smut resistance data obtained in (2) above, QTL analysis was carried out by the composite interval mapping (CIM) method using the QTL Cartographer gene analysis software (Wang S., C. J. Basten, and Z.-B. Zeng (2010). Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, N.C.). Upon analysis, the LOD threshold was determined to be 2.5. As a result, as shown in FIGS. 7 to 12, the presence of QTL regarding sugarcane smut resistance was confirmed in the following seven ranges: the range between markers N827337 and N821515 present in the 5th linkage group (August 18), the range between markers N826561 and N826906 present in the 17th linkage group (June 23, July 21, and August 18), and the range between markers N816552 and N821999 present in the 40th linkage group (July 21, August 18, and September 2) of the NiF8 sugarcane variety; the range between markers N915070 and N920207 present in the 1st linkage group (July 21, August 18, and September 2), the range between markers N914284 and N916129 present in the 13th linkage group (July 21, August 18, and September 2), and the range between markers N901177 and N900802 (June 23) and the range between markers N901524 and N918080 (June 23 and July 21) present in the 14th linkage group of the Ni9 sugarcane variety. Specifically, peaks exceeding the LOD threshold were observed in the above seven ranges. It was possible to specify the obtained peaks as shown in table 8, suggesting the presence of a causative gene (or a group of causative genes) having the function of causing the improvement of smut resistance at the each peak positions. In addition, the “Effect (%)” column in table 8 indicates an increase or a decrease in the incidence of smut. Therefore, if the value of “Effect (%)” is negative, it means that the QTL (quantitative trait locus) is linked to a trait characterized by the improvement of smut resistance. If the value of “Effect (%)” is positive, it means that the QTL is linked to a trait characterized by the reduction of smut resistance.

TABLE 8 Linkage Investigation Position Range LOD Effect Variety group date (cM) (cM) Close marker score (%) NiF8 5 8/18 3.8 18.7 N827337-N821515 2.6 8.2 NiF8 17 6/23 94.3 39.2 N826561-N826906 6.5 −16.5 NiF8 17 7/21 94.3 39.2 N826561-N826906 3.6 −10.1 NiF8 17 8/18 94.3 39.2 N826561-N826906 3.5 −9.7 NiF8 40 7/21 34.1 19.2 N816552-N821999 3.3 9.6 NiF8 40 8/18 34.1 19.2 N816552-N821999 3.0 8.9 NiF8 40 9/2  34.1 19.2 N816552-N821999 3.4 8.4 Ni9 1 7/21 5.5 32.0 N915070-N920207 2.8 −8.7 Ni9 1 8/18 5.5 32.0 N915070-N920207 2.6 −8.3 Ni9 1 9/2  5.5 32.0 N915070-N920207 3.3 −8.5 Ni9 13 7/21 12.9 39.5 N914284-N916129 2.6 8.3 Ni9 13 8/18 12.9 39.5 N914284-N916129 2.6 8.3 Ni9 13 9/2  12.9 39.5 N914284-N916129 2.6 7.4 Ni9 14_1 6/23 97.3 53.4 N901178-N900802 2.6 15.2 Ni9 14_2 6/23 137.7 38.0 N901524-N918080 5.2 −21.3 Ni9 14_2 7/21 137.7 38.0 N901524-N918080 4.7 −16.2

As shown in FIGS. 7 to 12, a marker located in the vicinity of the peak is inherited in linkage with a causative gene (or a group of causative genes) having the function of causing the improvement or reduction of smut resistance. This shows that the markers can be used as markers associated with resistance to sugarcane smut. Specifically, it has been revealed that the 85 types of markers shown in FIGS. 7 to 12 can be used as markers associated with resistance to sugarcane smut.

In addition, as examples of signals detected in 2 (6) above, table 9 shows signal levels of 14 types of markers among markers N827337 to N821515 present in the 5th linkage group of NiF8 for NiF8 and Ni9 and their progeny lines. In particular, the signal levels of N802870 are shown in FIG. 13.

TABLE 9 Linkage Marker group name NiF8 Ni9 F1 NiF8_5 N827337 1,629 529 1,354 344 439 403 1,330 1,593 1,823 1,495 1,717 512 495 739 N802879 4,193 393 2,706 370 347 372 1,484 2,319 1,707 1,897 1,803 365 518 389 N804818 3,093 591 2,173 531 494 408 2,480 3,233 3,589 4,092 4,075 533 635 613 N816296 1,489 379 1,440 510 358 342 1,445 1,822 1,671 1,664 1,691 355 396 336 N804607 2,125 375 1,454 393 361 394 1,258 1,266 1,422 1,416 1,311 660 382 495 N802870 5,498 828 4,275 377 412 444 5,198 4,496 4,195 4,631 4,207 446 655 361 N813249 6,034 778 4,329 553 498 764 4,208 3,754 3,864 3,749 3,330 627 711 414 N813609 2,821 701 2,178 750 901 869 2,820 3,222 3,729 2,888 3,552 566 945 840 N815502 2,044 481 2,452 806 493 436 2,390 2,587 2,088 2,211 2,088 493 640 425 N815101 2,055 446 2,660 549 419 344 3,184 2,673 3,153 3,105 3,116 504 347 346 N823481 2,096 509 1,200 457 487 393 1,629 1,460 1,870 1,925 1,920 528 585 402 N801028 6,877 907 5,694 886 799 651 5,083 3,359 3,578 4,019 4,197 792 377 930 N810798 5,506 633 5,171 823 608 513 5,720 4,545 5,463 6,279 5,907 561 847 775 N821515 3,768 819 3,190 790 489 418 4,899 3,485 3,282 3,331 3,603 553 921 515

Signal levels of 14 types of markers were found to be remarkably high for progeny lines exhibiting reduction of smut resistance among the linkage groups present in NiF8. These results also revealed that 14 types of markers among markers N827337 to N821515 present in the 5th linkage group can be used as markers associated with resistance to sugarcane smut.

Similarly, table 10 lists signal levels of 8 types of markers among markers N826561 to N826906 present in the 17th linkage group of NiF8 in NiF8 and Ni9 and the progeny lines. In particular, the signal levels of N827136 are shown in FIG. 14.

TABLE 10 Linkage Marker group name NiF8 Ni9 F1 NiF8_17 N826561 1,977 525 462 1,514 574 1,629 744 864 1,136 1,415 528 1,752 453 1,350 N827136 5,717 514 390 3,279 405 2,898 423 433 4,050 3,633 445 3,857 547 3,723 N826325 1,620 404 421 1,103 358 1,102 381 408 1,081 1,409 408 1,458 381 1,317 N803928 2,082 403 390 1,517 427 1,875 412 426 1,696 1,520 393 1,743 322 1,620 N822568 3,592 501 753 2,556 466 2,502 360 506 2,159 2,941 425 2,733 571 2,580 N829026 1,766 540 432 1,656 452 1,759 396 656 2,159 2,325 456 1,906 558 2,041 N815300 3,128 669 708 1,951 974 2,189 460 439 2,271 1,981 687 2,039 372 2,028 N826906 2,339 447 407 1,704 754 2,139 679 485 2,122 2,554 361 1,915 480 2,281

Signal levels of 8 types of markers were found to be remarkably high for progeny lines exhibiting excellent smut resistance among the linkage groups present in NiF8. These results also revealed that 8 types of markers among markers N826561 to N826906 present in the 17th linkage group can be used as markers associated with resistance to sugarcane smut.

Similarly, table 11 lists signal levels of 10 types of markers among markers N816552 to N821999 present in the 40th linkage group of NiF8 in NiF8 and Ni9 and the progeny lines. In particular, the signal levels of N812680 are shown in FIG. 15.

TABLE 11 Linkage Marker group name NiF8 Ni9 F1 NiF8_40 N816552 2,731 770 630 622 845 3,929 4,570 4,215 3,666 4,651 4,394 900 719 747 N827448 2,470 450 357 391 340 2,664 3,031 2,325 2,650 2,035 2,473 376 564 467 N829378 3,344 609 443 505 453 1,508 2,045 2,319 1,428 1,093 1,506 752 603 497 N829404 2,700 752 723 758 771 2,641 2,295 2,645 2,128 2,792 3,259 523 743 794 N828725 2,053 461 548 542 433 1,860 2,282 2,130 1,645 2,066 1,435 496 368 453 N812680 7,958 377 309 322 343 6,921 7,267 5,468 5,905 9,015 8,278 317 378 490 N811688 4,885 410 680 954 496 3,324 4,237 3,073 2,636 2,919 3,384 520 471 649 N819703 4,612 736 617 820 633 4,054 5,138 3,636 5,267 5,107 3,622 761 648 907 N815648 3,391 471 472 550 363 2,902 3,116 2,694 2,747 3,836 3,554 393 680 483 N821999 3,255 678 427 422 427 2,959 2,237 3,538 2,036 2,680 3,002 904 413 401

Signal levels of 10 types of markers were found to be remarkably high for progeny lines exhibiting reduction of smut resistance among the linkage groups present in NiF8. These results also revealed that 10 types of markers among markers N816552 to N821999 present in the 40th linkage group can be used as markers associated with resistance to sugarcane smut.

Similarly, table 12 lists signal levels of 19 types of markers among markers N915070 to N920207 present in the 1st linkage group of Ni9 in NiF8 and Ni9 and the progeny lines. In particular, the signal levels of N916081 are shown in FIG. 16.

TABLE 12 Linkage Marker group name NiF8 Ni9 F1 Ni9_1 N915070 424 1,195 418 1,393 1,122 1,717 480 1,356 1,359 1,707 370 424 424 403 N915209 560 1,796 435 2,840 1,776 3,016 601 2,376 2,361 3,451 446 541 462 484 N916186 496 2,002 403 2,447 1,808 1,571 415 2,608 1,723 2,687 406 671 466 432 N902342 372 1,245 349 1,049 1,003 1,045 420 1,062 1,346 2,206 333 352 401 398 N919949 625 1,459 406 2,169 1,942 2,723 738 1,679 2,360 3,490 650 680 444 572 N920597 450 4,702 399 5,028 3,819 5,583 348 6,733 4,669 7,196 436 431 393 537 N916081 516 13,678 954 16,011 14,893 10,082 634 10,528 10,441 11,232 504 785 435 604 N902047 955 5,233 858 4,400 3,853 4,711 825 3,373 5,336 6,194 581 992 555 854 N916874 491 3,320 486 2,511 2,869 3,276 708 2,304 3,046 4,073 416 791 409 430 N918161 438 2,109 411 1,989 1,892 2,109 397 1,690 2,193 2,643 406 610 398 335 N918538 372 1,059 508 1,229 1,293 1,368 487 1,253 1,704 1,967 511 423 395 381 N901676 648 1,534 702 2,407 1,395 1,389 705 1,590 1,820 1,918 521 577 483 582 N919743 635 2,361 437 1,703 1,731 1,990 471 2,385 2,076 3,665 568 417 399 398 N901176 697 5,017 408 3,009 5,027 5,059 820 5,316 3,362 3,347 764 454 715 420 N916035 757 4,444 684 3,088 3,803 3,576 580 4,310 4,270 4,272 448 585 485 581 N921010 521 5,630 448 6,214 5,012 7,792 909 5,074 4,902 5,904 557 658 559 611 N915835 424 7,875 538 12,542 10,900 15,388 568 9,698 10,501 14,732 391 505 400 469 N901348 493 3,188 558 6,692 7,451 6,486 805 3,553 7,406 2,655 659 584 638 438 N920207 421 5,291 349 4,550 4,857 6,695 385 1,962 3,567 11,697 449 478 416 450

Signal levels of 19 types of markers were found to be remarkably high for progeny lines exhibiting excellent smut resistance among the linkage groups present in Ni9. These results also revealed that 19 types of markers among markers N915070 to N920207 present in the 1st linkage group can be used as markers associated with resistance to sugarcane smut.

Similarly, table 13 lists signal levels of 11 types of markers among markers N914284 to N916129 present in the 13th linkage group of Ni9 in NiF8 and Ni9 and the progeny lines. In particular, the signal levels of N919839 are shown in FIG. 17.

TABLE 13 Linkage Marker group name NiF8 Ni9 F1 Ni9_13 N914284 439 1,102 380 551 1,358 562 1,234 1,463 1,247 877 1,235 492 467 1,342 N901453 788 1,511 661 638 1,120 560 1,380 2,056 2,671 807 1,415 512 533 1,821 N900044 688 1,693 646 652 1,600 554 1,632 2,841 2,410 618 1,619 603 577 1,639 N919839 389 4,719 364 329 4,261 332 4,331 6,387 5,540 360 4,307 352 334 7,400 N901567 426 2,890 374 399 3,213 526 3,981 5,253 5,212 434 3,364 449 383 4,346 N911103 500 902 388 424 1,069 414 1,246 2,352 1,465 408 1,036 417 630 1,500 N918508 686 5,836 513 667 4,963 778 4,317 7,106 5,911 599 4,037 587 547 7,786 N918344 385 1,970 352 578 1,765 470 2,000 3,298 2,428 409 2,079 426 483 2,488 N919696 497 2,696 496 427 2,327 685 1,928 2,433 2,370 414 2,043 680 657 2,763 N916172 471 1,960 448 378 3,025 445 2,990 4,282 3,314 433 2,666 403 445 3,518 N916129 526 5,026 641 506 3,393 858 3,465 5,094 5,261 478 4,030 383 558 6,621

Signal levels of 11 types of markers were found to be remarkably high for progeny lines exhibiting reduction of smut resistance among the linkage groups present in Ni9. These results also revealed that 11 types of markers among markers N914284 to N916129 present in the 13th linkage group can be used as markers associated with resistance to sugarcane smut.

Similarly, table 14 lists signal levels of 10 types of markers among markers N901178 to N900802 present in the 14th linkage group of Ni9 in NiF8 and Ni9 and the progeny lines. In particular, the signal levels of N918761 are shown in FIG. 18.

TABLE 14 Linkage Marker group name NiF8 Ni9 F1 Ni9_14_1 N901178 617 1,779 1,250 508 414 1,929 1,698 1,986 470 584 1,104 498 1,454 539 N918761 607 5,766 6,048 453 631 5,410 4,505 6,440 519 484 2,747 453 4,233 473 N913735 850 2,996 2,251 557 519 2,576 2,759 3,188 496 555 1,903 461 2,490 651 N900663 686 3,173 2,014 412 466 2,351 3,156 4,168 475 423 1,810 559 2,534 662 N918363 477 1,964 1,961 573 481 1,895 2,092 2,809 516 486 2,012 496 2,223 583 N918213 760 2,319 3,224 882 798 3,485 3,433 4,402 579 507 3,767 678 2,874 509 N900568 1,040 3,437 3,017 581 368 2,479 3,246 3,387 571 476 2,098 525 1,821 833 N912523 626 6,398 6,371 476 565 4,799 5,756 7,064 526 813 4,739 424 4,431 541 N900344 892 5,788 6,368 838 759 3,590 5,674 6,474 588 729 6,622 640 5,622 542 N900802 717 6,090 6,668 453 537 4,639 6,414 8,043 618 905 5,322 430 6,032 619

Signal levels of 10 types of markers were found to be remarkably high for progeny lines exhibiting reduction of smut resistance among the linkage groups present in Ni9. These results also revealed that 10 types of markers among markers N901178 to N900802 present in the 14th linkage group can be used as markers associated with resistance to sugarcane smut.

Similarly, table 15 lists signal levels of 13 types of markers among markers N901524 to N918080 present in the 14th linkage group of Ni9 in NiF8 and Ni9 and the progeny lines. In particular, the signal levels of N901160 are shown in FIG. 19.

TABLE 15 Linkage Marker group name NiF8 Ni9 F1 Ni9_14_2 N901524 428 2,677 2,763 425 457 343 2,534 1,954 617 445 3,083 1,291 2,532 674 N901163 379 3,462 2,099 909 861 632 3,268 3,426 600 380 3,196 3,202 3,260 392 N911063 575 4,326 5,570 385 466 384 2,738 7,453 398 409 7,625 8,794 2,220 381 N914692 625 3,592 4,016 811 577 419 3,574 3,955 742 959 3,573 4,756 4,094 714 N911405 386 1,893 1,692 470 404 411 1,715 2,402 411 437 1,762 2,052 1,660 396 N913383 580 2,923 2,202 710 421 596 2,256 2,986 821 798 2,768 3,336 2,062 708 N914112 564 3,387 3,390 825 417 730 1,913 3,528 1,000 987 2,934 3,753 2,600 966 N915180 537 2,482 2,950 566 485 396 2,590 2,968 438 497 2,242 3,021 3,110 729 N901160 452 4,333 6,165 375 394 333 4,340 6,432 424 417 7,227 8,545 4,069 359 N916293 560 2,069 1,908 725 868 520 1,420 3,179 463 517 1,720 2,129 1,681 464 N916263 414 2,358 1,775 379 348 359 2,136 2,174 522 404 2,041 1,850 2,502 491 N917579 485 2,335 1,873 501 459 395 2,208 3,210 440 390 2,959 1,816 3,724 378 N918080 469 1,238 1,171 432 532 361 1,621 1,567 380 402 1,269 1,015 1,940 442

Signal levels of 13 types of markers were found to be remarkably high for progeny lines exhibiting excellent smut resistance among the linkage groups present in Ni9. These results also revealed that 13 types of markers among markers N901524 to N918080 present in the 14th linkage group can be used as markers associated with resistance to sugarcane smut.

All publications, patents, and patent applications cited herein are incorporated herein by reference in their entirety. 

The invention claimed is:
 1. A method for producing a sugarcane line having improved smut resistance, said method comprising: extracting genomic DNA from a progeny plant obtained from parent plants, at least one of which is a sugarcane plant, and/or a genomic DNA of a parent sugarcane plant; determining by nucleic acid assay the presence of a marker associated with resistance to sugarcane smut in the obtained genomic DNA, and selecting the progeny plant as a plant having improved smut resistance based on the presence of said marker; and using the selected plant as a parent plant for crossing, to thereby produce progeny plant(s), wherein said marker consists of a continuous nucleic acid region in the obtained genomic DNA, and wherein said marker comprises at least 20 continuous nucleotides of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 74 to
 78. 2. The method for producing a sugarcane line according to claim 1, wherein a DNA chip that comprises a probe corresponding to the marker associated with resistance to sugarcane smut is used in the determination step.
 3. The method for producing a sugarcane line according to claim 1, wherein the progeny plant used in said genomic DNA extracting step is in the form of seeds or a young seedling, and the genomic DNA is extracted from the seeds or the young seedling.
 4. The method for producing a sugarcane line according to claim 1, wherein the progeny plant(s) produced using the selected plant as a parent plant for crossing is in the form of seeds or a young seedling. 